Light source alignment is necessary for efficient generation of product ions and minimization of noise (e.g., due to photo-desorption and photo-ionization from instrument surfaces) in ultraviolet light (λ<400 nm, e.g., 213 nm) photo-dissociation (UVPD) and infrared multiphoton dissociation (IRMPD) mass spectrometry. Alignment of the light source is typically achieved by placement of two or more target apertures along the light path. Light source adjustment is performed until the light is sufficiently centered along the light path at each target, thereby ensuring that the light source is aligned such that the light beam is coaxial with the ion storage location and/or ion beam path in the mass spectrometer. Initial coarse alignment using target apertures needs to be achieved while the mass spectrometer system is at atmospheric pressure and partially disassembled. UVPD, however, takes place in vacuo within the mass spectrometer, and therefore the system needs to be evacuated to test the alignment of the light beam, perhaps requiring several cycles of venting, disassembly, and evacuation of the mass spectrometer if the initial alignment is not satisfactory, further adding to the system down time. In addition, photo-dissociation experiments performed under such ex vacuo alignment conditions may lead to suboptimal performance.
Therefore, there is a need for a method of aligning a light beam within a mass spectrometer that reduces or eliminates the problems described above.